Partition Function for Two Hybridized Sequences

Partition Function Cofolding. More...

Detailed Description

Partition Function Cofolding.

To simplify the implementation the partition function computation is done internally in a null model that does not include the duplex initiation energy, i.e. the entropic penalty for producing a dimer from two monomers). The resulting free energies and pair probabilities are initially relative to that null model. In a second step the free energies can be corrected to include the dimerization penalty, and the pair probabilities can be divided into the conditional pair probabilities given that a re dimer is formed or not formed. See [2] for further details.

As for folding one RNA molecule, this computes the partition function of all possible structures and the base pair probabilities. Uses the same global pf_scale variable to avoid overflows.

After computing the partition functions of all possible dimeres one can compute the probabilities of base pairs, the concentrations out of start concentrations and sofar and soaway.

Dimer formation is inherently concentration dependent. Given the free energies of the monomers A and B and dimers AB, AA, and BB one can compute the equilibrium concentrations, given input concentrations of A and B, see e.g. Dimitrov & Zuker (2004)

Collaboration diagram for Partition Function for Two Hybridized Sequences:

Files
file	concentrations.h
	Concentration computations for RNA-RNA interactions.
file	part_func_up.h
	Implementations for accessibility and RNA-RNA interaction as a stepwise process.

Typedefs
typedef struct vrna_dimer_pf_s	vrna_dimer_pf_t
	Typename for the data structure that stores the dimer partition functions, vrna_dimer_pf_s, as returned by vrna_pf_dimer()
typedef struct vrna_dimer_pf_s	cofoldF
	Backward compatibility typedef for vrna_dimer_pf_s.

Variables
int	mirnatog
	Toggles no intrabp in 2nd mol.
double	F_monomer [2]
	Free energies of the two monomers.
typedef struct vrna_dimer_conc_s	vrna_dimer_conc_t
	Typename for the data structure that stores the dimer concentrations, vrna_dimer_conc_s, as required by vrna_pf_dimer_concentration()
typedef struct vrna_dimer_conc_s	ConcEnt
	Backward compatibility typedef for vrna_dimer_conc_s.
vrna_dimer_conc_t *	vrna_pf_dimer_concentrations (double FcAB, double FcAA, double FcBB, double FEA, double FEB, const double *startconc, const vrna_exp_param_t *exp_params)
	Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers. More...

Simplified global partition function computation using sequence(s) or multiple sequence alignment(s)
vrna_dimer_pf_t	vrna_pf_co_fold (const char *seq, char *structure, vrna_ep_t **pl)
	Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers. More...

Function Documentation

vrna_dimer_pf_t vrna_pf_co_fold	(	const char *	seq,
		char *	structure,
		vrna_ep_t **	pl
	)

#include <ViennaRNA/part_func.h>

Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers.

This simplified interface to vrna_pf_dimer() computes the partition function and, if required, base pair probabilities for an RNA-RNA interaction using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing.

Note

In case you want to use the filled DP matrices for any subsequent post-processing step, or you require other conditions than specified by the default model details, use vrna_pf_dimer(), and the data structure vrna_fold_compound_t instead.

See also

vrna_pf_dimer()

Parameters

seq	Two concatenated RNA sequences with a delimiting '&' in between
structure	A pointer to the character array where position-wise pairing propensity will be stored. (Maybe NULL)
pl	A pointer to a list of vrna_ep_t to store pairing probabilities (Maybe NULL)

Returns

vrna_dimer_pf_t structure containing a set of energies needed for concentration computations.

vrna_dimer_conc_t* vrna_pf_dimer_concentrations	(	double	FcAB,
		double	FcAA,
		double	FcBB,
		double	FEA,
		double	FEB,
		const double *	startconc,
		const vrna_exp_param_t *	exp_params
	)

#include <ViennaRNA/concentrations.h>

Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers.

This function takes an array 'startconc' of input concentrations with alternating entries for the initial concentrations of molecules A and B (terminated by two zeroes), then computes the resulting equilibrium concentrations from the free energies for the dimers. Dimer free energies should be the dimer-only free energies, i.e. the FcAB entries from the vrna_dimer_pf_t struct.

Parameters

FcAB	Free energy of AB dimer (FcAB entry)
FcAA	Free energy of AA dimer (FcAB entry)
FcBB	Free energy of BB dimer (FcAB entry)
FEA	Free energy of monomer A
FEB	Free energy of monomer B
startconc	List of start concentrations [a0],[b0],[a1],[b1],...,[an][bn],[0],[0]
exp_params	The precomputed Boltzmann factors

Returns

vrna_dimer_conc_t array containing the equilibrium energies and start concentrations